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My Macbook Pro will only boot into recovery after upgrading Disk Utility from the App Store. In the Disk Utility in Recovery Mode, my disk can't be checked for errors and it cannot unmount. (I believe it also recognizes the existence of the filesystem but cannot verify it or something similar) I have taken the hard drive out of my device and used a disk enclosure and can view my files. How can I copy these files to another HD/SSD and boot from it (successfully) into macOS? I have a file encryptor that encrypts some of my files so I'd need all my app/file data to remain when I copy the files and boot the drive.

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Have a look at Carbon Copy Cloner: https://bombich.com/, it allows you to create bootable copies of your internal HDD.

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